Land-based management has reduced nutrient discharges; however, many coastal waterbodies remain impaired. Oyster "bioextraction" of nutrients and how oyster aquaculture might complement existing management measures in urban estuaries was examined in Long Island Sound, Connecticut. Eutrophication status, nutrient removal, and ecosystem service values were estimated using eutrophication, circulation, local- and ecosystem-scale models, and an avoided-costs valuation. System-scale modeling estimated that 1.31% and 2.68% of incoming nutrients could be removed by current and expanded production, respectively. Up-scaled local-scale results were similar to system-scale results, suggesting that this up-scaling method could be useful in bodies of water without circulation models. The value of removed nitrogen was estimated using alternative management costs (e.g., wastewater treatment) as representative, showing ecosystem service values of $8.5 and $470 million per year for current and maximum expanded production, respectively. These estimates are conservative; removal by clams in Connecticut, oysters and clams in New York, and denitrification are not included. Optimistically, the calculation of oyster-associated removal from all leases in both states (5% of bottom area) plus denitrification losses showed increases to 10%-30% of annual inputs, which would be higher if clams were included. Results are specific to Long Island Sound, but the approach is transferable to other urban estuaries.